GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Bap2 in Pseudomonas simiae WCS417

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate GFF295 PS417_01505 gamma-aminobutyrate transporter

Query= TCDB::Q2VQZ4
         (536 letters)



>lcl|FitnessBrowser__WCS417:GFF295 PS417_01505 gamma-aminobutyrate
           transporter
          Length = 463

 Score =  233 bits (594), Expect = 1e-65
 Identities = 144/392 (36%), Positives = 204/392 (52%), Gaps = 10/392 (2%)

Query: 33  LKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCLALAEM 92
           L+Q LK RH+ M++I G IGAGLFVGSG A+   GPA LL  Y   G +++     LAEM
Sbjct: 10  LEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLL-AYAAAGTLVVLVMRMLAEM 68

Query: 93  AVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWREDINMAV 152
           AV  P  G+F TY  R +    GF +GW Y   W+ V+P E  AA+  +  W  DI + V
Sbjct: 69  AVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAWFPDIAIWV 128

Query: 153 WVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQGYIGVKY 212
           +  V  ++L    +F V+ YGE EF  ++IK+ A VGF+ILG+    G +      GV +
Sbjct: 129 FTLVITLLLTATNLFSVKNYGEFEFWFALIKVVAIVGFVILGLAAIFGFLPTSQVSGVSH 188

Query: 213 WRDPGAF--TSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFWRIAIF 270
             D   F         A  +   FSF GTE+V +AAAES NP + I  A+  V WRI +F
Sbjct: 189 LFDTQGFMPNGMGAVLAAILTTMFSFMGTEIVTIAAAESKNPGQQITKATNSVIWRIGLF 248

Query: 271 YILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVAVLSVA 330
           Y+L++FIV  ++P NDP L       T        ++  GI     I++ V+ VAV S  
Sbjct: 249 YLLSIFIVVSLVPWNDPTLAAVGSYQT-------VLERMGIPNAKLIVDLVVLVAVTSCL 301

Query: 331 NSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQGMEIFG 390
           NS  + ++R + ++  R  AP   K  +  G P + V+L      LA          +F 
Sbjct: 302 NSALYTASRMLFSLGRRGDAPAVAKRTNKSGTPYWAVLLSTGAAFLAVFANYVAPAAVFE 361

Query: 391 WLLALTGLGFLFVWGSICLAHIRMRAGMKAQG 422
           +LLA +G   L V+  I ++ +RMR    A G
Sbjct: 362 FLLASSGAIALLVYLVIAVSQLRMRQKRTAAG 393


Lambda     K      H
   0.327    0.142    0.442 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 578
Number of extensions: 30
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 536
Length of database: 463
Length adjustment: 34
Effective length of query: 502
Effective length of database: 429
Effective search space:   215358
Effective search space used:   215358
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory